DNA sequencing

ABSTRACT

A method for sequencing a strand of DNA, including the steps of: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with a deoxyribonucleoside triphosphate, a DNA polymerase, and a chain terminating agent under conditions in which the polymerase causes the primer to be elongated to form a series of DNA products differing in length of the elongated primer, each DNA product having a chain terminating agent at its elongated end; the number of each DNA product being approximately the same for substantially all DNA products differing in length from 1 to 20 bases.

BACKGROUND OF THE INVENTION

This invention was made with government support including a grant fromthe U.S. Public Health Service, contract number AI-06045. The U.S.government has certain rights in the invention.

This invention relates to DNA sequencing and in particular to automatedmethods for DNA sequencing.

DNA sequencing is generally carried out by the method of Sanger et al.(Proc. Nat. Acad. Sci. USA 74:5463, 1977) and involves enzymaticsynthesis of single strands of DNA from a single stranded DNA templateand a primer. Referring to FIG. 1, four separate syntheses are carriedout. A single stranded template is provided along with a primer whichhybridizes to the template. The primer is elongated using a DNApolymerase, and each reaction terminated at a specific base (guanine, G,adenine, A, thymine, T, or cytosine, C) via the incorporation of anappropriate chain terminating agent, for example, a dideoxynucleotide.Enzymes currently used for this method of sequencing include: the largefragment of Escherichia coli DNA polymerase I ("Klenow" fragment),reverse transcriptase, Taq polymerase, and a modified form ofbacteriophage T7 DNA polymerase.

Still referring to FIG. 1, the four DNA synthesis reactions result information of four series of DNA products, each product having onedefined terminus and one variable terminus. The defined terminus startswith the primer molecule. The variable terminus ends with a chainterminating agent specific for the nucleotide base (either G, A, T, orC) at which the synthesis reaction terminated. The four different seriesof products are each separated on the basis of their molecular weight,in four separate lanes in a high resolution polyacrylamide gel, to formfour series of bands, with each band on the gel correspondingsequentially to a specific nucleotide in the DNA sequence. Thus, therelative positions of the bands identify the positions in the DNAsequence of each given nucleotide base. Generally, the DNA products arelabelled so that the bands produced are readily detected. As shown inFIG. 1, the intensity of the bands is generally non uniform, within asingle lane, because band intensity is directly related to the totalnumber or concentration of DNA products of the same molecular weight ina specific lane, and this number varies from one product to another evenwhen they are of approximately the same molecular weight and even whenthey contain the same chain terminating agent.

Using the above methodology, automated systems for DNA sequence analysishave been developed. One instrument, manufactured by EG&G, uses a ³²P-label and a DNA polymerase, and the resulting DNA products separatedby gel electrophoresis. Toneguzzo et al , 6 Biotechniques 460, 1988. A³² P-detector at the bottom of the gel scans for radioactivity as itpasses through the bottom of the gel Four synthesis reactions arerequired for each template to be sequenced, as well as four lanes oneach gel, a separate lane being used for products terminated by eachspecific chain terminating agent, as shown for example in FIG. 1.

Kanbara et al , 6 Biotechnology 816, 1988, have replaced the ³²P-labelled primer, described above, with a fluorescent-labelled primerThe resulting fluorescently labelled products are excited with a laserat the bottom of the gel and the fluorescence detected with a CRTmonitor. This procedure also requires four synthesis reactions and fourlanes on the gel for each template to be sequenced.

Applied Biosystems manufactures an instrument in which four differentprimers are used, each labelled with a different fluorescent marker.Smith et al., 13 Nuc. Acid. Res. 2399, 1985; and 321 Nature 674, 1986.Each primer is used in a separate reaction containing one of fourdideoxynucleotides. After the four reactions have been carried out theyare combined together and run in a single lane on a gel. A laser at thebottom of the gel is used to detect fluorescent products after they havebeen permeated or electrophoresed through the gel. This system requiresfour separate annealing reactions and four separate synthesis reactionsfor each template, but only a single lane on the gel. Computer analysisof the sequence is made easier by having all four bands in a singlelane.

DuPont provides an instrument in which a different fluorescent marker isattached to each of four dideoxynucleoside triphosphates. Prober et al.,238 Science 336, 1987. A single annealing step, a single polymerasereaction (containing each of the four labelled dideoxynucleosidestriphosphates) and a single lane in the sequencing gel are required. Thefour different fluorescent markers in the DNA products are detectedseparately as they are electrophoresed through the gel.

Englert et al., U S. Pat. No. 4,707,237 (1987), describes a multichannelelectrophoresis apparatus having a detection means, disposedsubstantially across the whole width of the gel, which can senselabelled DNA products as they migrate past the detector means in fourseparate lanes, and identifies the channel or lane in which the sampleis located. Preferably, radioisotopic labels are used.

Inherent to procedures currently used for DNA sequence analysis is thenecessity to separate either radioactively or fluorescently-labelled DNAproducts by a gel permeation procedure such as polyacrylamide or othergel electrophoresis, and then detect their locations relative to oneanother along the axis of permeation or movement through the gel. Theaccuracy of this procedure is determined in part by the uniformity ofthe signal in bands which have permeated approximately the same distancethrough the gel. Differences or variations in signal intensities betweennearby bands create several problems. First, they decrease thesensitivity of the method, which is limited by the ability to detect thebands containing the weakest signals. Second, they create difficultiesin determining whether a band with a weak signal is a true signal due tothe incorporation of a chain terminating agent, or an artifact due to apause site in the DNA, where the polymerase has dissociated. Third, theydecrease the accuracy in determining the DNA sequence between closelyspaced bands since the strong signal of one band may mask the weaksignal of its neighbor.

SUMMARY OF THE INVENTION

All of the foregoing problems are overcome in the present invention,where approximately the same amounts of DNA products of similarmolecular weights are produced in a sequencing reaction, and thus nearbybands in the sequencing gel, in the same lane, are of approximately thesame intensity.

The ability to produce nearby bands of approximately the same intensityis useful since it permits the results of any sequencing reaction to beread more easily and with greater certainty. Further, since the DNAproducts from a sequencing reaction with a specific chain terminatingagent form bands which are of approximately the same intensity as thatof nearby bands, band intensity itself provides a specific label for theseries of bands so formed. The number of DNA products of approximatelythe same molecular weight produced by a given chain terminating agentvaries depending upon the concentration of the chain terminating agent.Thus, by using a different concentration of each of the four chainterminating agents for the synthesis, the DNA products incorporating onechain terminating agent are distinguished from DNA products ofapproximately the same molecular weight incorporating other chainterminating agents in that they differ in number or amount;consequently, the bands of DNA products can be identified as to chainterminating agent simply by their intensity as compared to theintensities of nearby bands. As a result, two or more series of DNAproducts, each series having a different chain terminating agent, can besubjected to gel permeation in a single lane and identified, i.e.,distinguished from each other, by the intensity of each band as comparedto the intensity of nearby bands. Moreover, the syntheses of DNAproducts incorporating different chain terminating agents need not becarried out separately, in separate containers, but may all be carriedout simultaneously in a single reaction vessel, and the same label,e.g., radioisotopic, fluorescent, etc. can, if desired, be used for allchain terminating agents instead of a different label for each, thussimplifying the procedure.

It should be noted, however, that there is a gradual decrease inintensity of all bands of DNA products as they permeate through the gel,those that have travelled the shortest distance displaying lessintensity than those which have travelled the farthest distance.Neverless, the relative intensity of each band as compared to nearbybands at any location along the axis of permeation remains approximatelythe same throughout. This conservation of relative intensity throughoutthe extent of permeation makes possible the present invention.

By "nearby bands" is meant those in the same lane within about 20-30 mmeither ahead of or behind the band in question, measured along the axisof permeation. In general, the nearby bands include DNA productsdiffering from the one in question by no more than 20 bases (i.e., witha mass differing by no more than about 6,000 daltons).

In general, the invention features a DNA polymerase for use in DNAsequencing reactions, which, in a sequencing reaction, causes DNAproducts of slightly different molecular weight to be produced inapproximately equal numbers. Thus, when such DNA products are separatedin a gel matrix they form bands, with nearby bands being ofapproximately the same intensity. Without being bound to any particulartheory, the inventors regard this uniformity in intensity as being dueto the polymerase not discriminating between normal nucleosidetriphosphates and chain terminating agents, such as dideoxynucleosidetriphosphates.

In a first aspect, the invention features a method for sequencing astrand of DNA, including the steps of: providing the strand of DNA;annealing the strand with a primer able to hybridize to the strand togive an annealed mixture; incubating the annealed mixture with adeoxyribonucleoside triphosphate, a DNA polymerase, and a first chainterminating agent under conditions in which the polymerase causes theprimer to be elongated to form a first series of first DNA productsdiffering in length of the elongated primer, each first DNA producthaving a chain terminating agent at its elongated end; the number ofeach first DNA product being approximately the same for substantiallyall DNA products differing in length from 1 to 20 bases. Preferably, themethod further includes the steps of: separating the first DNA productsby gel permeation according to molecular weight to form a first seriesof bands, each first series band representing a first DNA product of agiven molecular weight, wherein the intensity of each nearby firstseries band is approximately the same for substantially all first seriesbands; and determining the position of each first band.

By "substantially all" is meant that at least 9 out of 10 (or 19 out of20) nearby bands have approximately the same intensity. That is, onlyoccasional bands will have a different intensity. This differentintensity results from artifacts. One example of such an artifact is thecompression of two or more DNA products of different molecular weightwithin one band. The result of two such compressions are shown in FIG. 2where the artifactual bands are marked with an asterisk. Byapproximately the same is meant that band intensity varies by at most 2fold, most preferably at most 1.2 fold. By gel permeation is meant toinclude existing polyacrylamide gels used for DNA sequencing, and anyother mechanism for separating DNA products according to their molecularweight.

In one embodiment, production of nearby bands of approximately the sameintensity is achieved by incubating a DNA polymerase in a solutioncontaining manganese or iron ions.

In one preferred embodiment, the method further includes the steps ofproviding a second chain terminating agent in the annealed mixture at aconcentration different from the first chain terminating agent, whereinthe DNA polymerase causes production of a second series of second DNAproducts, each second DNA product having the second chain terminatingagent at its elongated end, the number of each second DNA product beingapproximately the same for substantially all DNA products differing inlength from 1 to 20 bases, wherein the number of substantially all thefirst and all the second DNA products differing in length from 1 to 20bases is distinctly different. Most preferably, the second series ofsecond DNA products form a second series of bands when separated by gelpermeation according to molecular weight, wherein the intensity ofsubstantially all nearby second series bands is approximately the same,and the intensity of substantially all bands of the first series isdistinctly and distinguishably different from the intensity of eachnearby band of the second series, and the method further includes thestep of determining the position- and intensity of each band, theintensity being representative of a particular band series.

By distinctly different is meant that a band of one series can bedistinguished from a nearby band (i.e., a band with a length differingfrom 1 to 20 bases) in the other series. That is, a machine whichmeasures the number of DNA products of a specific molecular weight candistinguish the two series of DNA products from each other.

In another preferred embodiment, the method includes providing two otherchain terminating agents wherein the polymerase causes production of asecond and third series of second and third DNA products, the number ofeach second and third DNA products being approximately the same forsubstantially all DNA products differing in length from 1 to 20 bases,wherein the number of substantially all the first, all the second andall the third DNA products differing in length from 1 to 20 bases isdistinctly different. Most preferably, each second and third series ofthe second and third DNA products form a different series of second andthird bands, when separated by gel permeation according to molecularweight, wherein the intensity of substantially all nearby second seriesbands is approximately the same, the intensity of substantially allnearby third series bands is approximately the same, and wherein theintensity of substantially all nearby bands of different series isdistinctly different; and the method further includes the steps ofdetermining the position and intensity of each band, the intensity beingrepresentative of a particular band series.

In yet another preferred embodiment, the method includes providing inthe annealed mixture four different deoxyribonucleoside triphosphatesand four different chain terminating agents, wherein the DNA polymerasecauses production of second, third and fourth series of second, thirdand fourth DNA products, the number of each second, third and fourth DNAproducts being approximately the same for substantially all DNA productsdiffering in length from 1 to 20 bases, wherein the number ofsubstantially all the first, all the second, all the third and all thefourth DNA products differing in length from 1 to 20 bases is distinctlydifferent. Most preferably, each second, third and fourth series produceseries of second, third and fourth bands, when separated by gelpermation according to molecular weight, wherein the intensity ofsubstantially all nearby second series bands, or substantially allnearby third series bands, or substantially all nearby fourth seriesbands is approximately the same, and wherein the intensity ofsubstantially all nearby bands in a different series is distinctlydifferent; most preferably, the method further includes the steps ofdetermining the position and intensity of each band, the intensity beingrepresentative of a particular band series.

In other preferred embodiments, the annealed mixture is provided with amanganese or iron ion, wherein the ion causes the polymerase to benon-discriminatory for a chain terminating agent; the DNA products areseparated according to molecular weight in less than four lanes of agel; the intensity of each band is measured by a gel reading apparatus;the DNA polymerase is chosen from a T7-type DNA polymerase, the largefragment of E. coli DNA polymerase I, and Taq polymerase; and the chainterminating agent is a dideoxynucleoside triphosphate.

In related aspects, the invention features a method for sequencing astrand of DNA, including the steps of either (a) providing a DNApolymerase, and incubating the polymerase and the strand of DNA in asolution including an ion of manganese or iron and a chain terminatingagent; or (b) providing a DNA polymerase which is substantiallynon-discriminating for a chain terminating agent.

In another related aspect, the invention features a method for producinga DNA polymerase for DNA sequencing, including the step of mixing theDNA polymerase in a solution including a manganese or iron ion.

In another aspect, the invention features a solution including a T7-typeDNA polymerase, or a Taq polymerase, and a manganese or iron ion.Preferably the ion is at a concentration from 0.005 to 100 millimolar.

In another aspect, the invention features a kit for sequencing DNAhaving a DNA polymerase, a chain terminating agent, and a manganese oriron ion.

In preferred embodiments, the polymerase is a T7-type DNA polymerase,the large fragment of E. coli DNA polymerase I, or Taq polymerase; thechain terminating agent is a dideoxynucleotide; and the kit furtherincludes a deoxyribonucleoside triphosphate.

In another aspect, the invention features a method for automatedsequencing of DNA including providing a polymerase which issubstantially non-discriminating for a chain terminating agent andcauses production of a series of DNA products differing in molecularweight and terminating with the same chain terminating agent, whereinthe DNA products produce substantially all nearby bands of approximatelythe same intensity.

By substantially non-discriminating is meant that chain terminatingagents are incorporated uniformly along the length of the DNA,regardless of the DNA sequence. By approximately the same is meant thatthe intensity differs by at most two- to three-fold.

In another aspect, the invention features an automated DNA sequencingapparatus having a reactor for providing at least two series of DNAproducts formed from a single primer and a DNA strand, each DNA productof a series differing in molecular weight and having a chain terminatingagent at one end; separating means for separating the DNA products toform a series of bands, the intensity of substantially all nearby bandsin a series being approximately the same, and the intensity ofsubstantially all nearby bands in a different series being different,band reading means for determining the position and intensity of eachband after separating; and computing means for determining the DNAsequence of the DNA strand directly from the position and intensity ofthe bands.

In preferred embodiments, the reactor includes a manganese or iron ion,and a T7-type DNA polymerase.

In another aspect, the invention features a solution or kit including apyrophosphatase, a DNA polymerase, and a chain terminating agent ordITP; and a method for DNA sequencing, including providingpyrophosphatase in the sequencing reaction. Inclusion of pyrophosphatasein a sequencing reaction reduces the level of pyrophosphate and improvesthe uniformity of band intensity of nearby bands.

In any of the above aspects, the manganese or iron ion may be providedin the presence of a chelate, such as citrate or isocitrate. Suchchelates are thought to provide a more controlled level of the desiredion in a DNA sequencing reaction.

In a final aspect, the invention features a T7 DNA polymerase Δ Lys118--Arg 145, and DNA encoding this polymerase. This polymerase has nodetectable exonuclease activity.

We have found conditions under which DNA polymerases can be modified tochange their ability to incorporate a chain terminating agent at theelongating terminus of a primer DNA in the presence of a DNA template.This ability allows DNA sequencing to be performed with lowerconcentrations of chain terminating agents, thus greatly lowering thecosts of a DNA sequencing reaction. Further, we have found that DNApolymerases having this ability produce nearby bands in a sequencing gelwhich are of approximately uniform intensity. That is, the polymerase isno longer discriminating, to any great extent, between incorporatingchain terminating agents and normal deoxynucleoside triphosphates. Wehave shown that at least three polymerases can be modified in this way,including a modified T7 DNA polymerase, the large fragment of E. coliDNA polymerase I, and Taq polymerase. Other polymerases having homologyto these polymerases will also work in the invention.

Another advantage of this invention is that the concentration of anygiven chain terminating agent to be used in a sequencing reaction isreadily calculated, since band intensity is directly related to theconcentration of any chain terminating agent and is the same for eachsuch agent.

The modified polymerases of this invention are particularly useful inDNA sequencing reactions since only a single sequencing reactioncontaining all four chain terminating agents at four differentconcentrations is necessary. Thus, less than four different sequencingreactions can be used for any particular DNA template.

Other features and advantages of the invention will be apparent from thefollowing description of the preferred embodiments thereof, and from theclaims.

Description of the Preferred Embodiments

The drawings will first briefly be described.

DRAWINGS

FIG. 1 is a schematic representation of DNA sequencing by the method ofSanger et al., supra.

FIGS. 2-7 are graphical representations of relative band intensities ofsix different sequencing gels scanned by an Applied Biosystems Model370A DNA Sequencing System, each from a single gel lane containing asequencing reaction mixture resulting from using a genetically modifiedT7 DNA polymerase in the presence of various mixtures of manganese ormagnesium and various dideoxynucleosides.

In each of these Figures, the DNA sequenced was mGPl-2 (encoding T7 RNApolymerase, Tabor et al., Proc. Nat. Acad. Sci. USA, 84:4767, 1987), andthe primer was the fam primer of Applied Biosystems. In each case theunprocessed (raw) output for the fam primer is shown. The start and endof each output are indicated. In addition, the positions of thesequences are shown, with respect to their corresponding position inwild type T7 DNA. (Dunn et al., J. Mol. Biol. 8:452, 1983) The points oneach graph marked by an asterisk represent regions of compression, whereat least two DNA products of different molecular weight migrate at thesame position on the gel. Compressions are generally described by Taboret al., Proc. Nat. Acad. Sci. USA, 84 4767, 1987.

FIG. 8 is a graph showing the optimum concentration of magnesium andmanganese for DNA polymerase activity for a genetically modified T7 DNApolymerase in the presence and absence of 4.0 mM isocitrate.

FIG. 9 is a graph showing the effect of different concentrations ofisocitrate in the presence of 10 mM magnesium or manganese on DNApolymerase activity for a genetically modified T7 DNA polymerase.

FIG. 10 is a schematic map of pGP5 8, a plasmid that encodes for agenetically modified T7 DNA polymerase lacking amino acids Lys 118through Arg 145, that lacks exonuclease activity.

FIG. 11 is a diagrammatic representation of an automatic sequencingapparatus of this invention.

DNA Polymerase

DNA polymerases useful in this invention include those belonging to aclass of homologous polymerases including T7 type DNA polymerases (suchas T7, T3, ΦI, ΦII, H, W31, gh-l, Y, All22, or SP6), the large fragmentof E. coli DNA polymerase I and Taq polymerase. By homologouspolymerases is meant an enzyme that discriminates againstdideoxynucleoside triphosphates compared to deoxynucleosidetriphosphates in the presence of magnesium; however, when magnesium isreplaced by manganese the discrimination against dideoxynucleosidetriphosphates is reduced. These polymerases are used in a DNA sequencingreaction under conditions in which they produce nearby bands ofapproximately uniform intensity (with about a 1.5- to 2.0-fold variationin intensity) when the DNA products of the sequencing reaction are runin a gel. By nearby is meant to include bands representing DNA productsof molecular weight differing by as much as 6000, i.e., 20 bases. Theactual value of this intensity will decrease along the length of thegel, as described below and shown in the Figures. Band intensityreflects the number of DNA products within a certain band. Labels, suchas fluorophores or radioisotopes, are used to produce a readilydetectable band of intensity reflective of the number of such DNAproducts. Thus, in this invention, nearby bands derived from onesequencing reaction with one chain terminating agent have approximatelythe same number of DNA products and thus a uniform band intensity. Thesequencing conditions include incubation of the polymerase in thepresence of specific divalent or trivalent cations such as manganese (IIand III), ferrous and ferric ions; monovalent and divalent cations whichhave no detectable effect, or are detrimental to DNA synthesis, include:K, Na, Ba, Be, Ca, Ce, Cr, Co, Cu, Ni, Si and Zn. The anion isunimportant, for example, chloride, acetate, and sulfate are suitable.Under these conditions the requirement for chain terminating agents,such as dideoxynucleosides, is lessened by almost 1000-fold for enzymessuch as large fragment of E. coli DNA polymerase I and Taq polymerase,and by about 10-fold for a modified T7 polymerase. A chelator may alsobe provided in this solution in order to help regulate the concentrationof available divalent metal ions. For example, citrate or isocitrate maybe provided. These chelates are thought to maintain the level of, forexample, free manganese ions at a concentration of between 10 and 100 μMover a wide range of manganese concentrations. That is, the chelatoracts as a buffer.

The DNA polymerases of this invention do not discriminate significantlybetween dideoxynucleoside analogs and deoxynucleosides along the lengthof the DNA template. That is, in the presence of manganese or iron thesepolymerases are unable to discriminate between a nucleotide that has a3' hydroxyl group versus one that does not (i.e., has two hydrogens atthe 3' position of the ribose). However, these polymerases dodiscriminate against modifications at other positions on thenucleosides, even in the presence of manganese or iron. For example, thepolymerases do discriminate against some dideoxynucleoside analogs whichhave fluorescent groups attached compared to deoxynucleosides. However,the polymerase do not discriminate to a different extent at neighboring,or nearby nucleotides, on the basis of the presence or absence of themodification to the dideoxynucleoside. Thus, while they discriminatestrongly against these analogs, requiring higher concentrations for aDNA sequencing reaction compared to unmodified dideoxynucleosides, theintensity of nearby bands will still be uniform. For example, there is a10 fold discrimination against dideoxy ITP (ddITP), compared to dideoxyGTP (ddGTP), in the presence of Mn However, all the bands produced in asequencing reaction are of equal intensity with ddITP since there is nodifferential discrimination along the length of the DNA template.

Thus, the polymerases of this invention provide a uniform efficiency ofincorporation of chain terminating agents, even if they discriminateagainst overall incorporation.

Chain terminating agents useful in this invention includedideoxynucleosides having a 2', 3' dideoxy structure. Other agentsuseful in the invention are those able to specifically terminate a DNAsequencing reaction at a specific base, and are not discriminatedagainst by the polymerase under the above conditions.

In order to determine whether any particular DNA polymerase, incombination with any particular chain terminating agent, or othercomponent of a sequencing reaction mixture, is useful in this invention,a standard sequencing reaction is performed, as described below andshown in the drawings, and the extent of band formation, and theuniformity of nearby bands in a sequencing gel, reviewed. If thepolymerase reaction does not extend the primer by at least 20 bases, itis not suitable under the conditions used. Adjacent band uniformitywithin a two-fold or less range is useful in this invention, preferablythe uniformity is within a 1.0-1.5 fold range. Similarly, determinationof optimum cation concentration, or of other potential cations useful inthe invention, is determined by use of this sequencing reaction undervarious conditions. For example, cations are tested in ranges from0.005-100 mM. An example of such an experiment follows:

DNA synthesis is measured using a 17-mer primer of sequence5'-GTAAAACGACGGCCAGT-3' (New England Biolabs catalog number 1211) thathas been labeled with ³² P at its 5' end and annealed to single-strandedmGPl-2 DNA. Tabor et al., proc. Nat. Acad. Sci. USA 84:4767 (1987) andTabor et al., J. Biol. Chem. 262:16212 (1987). Any other template isequally useful in this reaction. This primer-template is used in areaction that contains a DNA polymerase in the presence of a range ofconcentrations of a metal ion. Reactions are carried out in the presenceof a given concentration of all 4 deoxynucleotides (dNTPS, 20-200 μM),and over a range of concentrations of one dideoxynucleotide (ddNTP, inthis example, ddGTP from 10-500 μM). The DNA products are then analyzedby polyacrylamide gel electrophoresis, where DNA synthesis is detectedas extensions of the primer producing bands, representing extensions ofvarious molecular weights, in the gel.

In a specific example, each reaction mixture (10μl) contained 0.1 μg³²P-primer-template, 40 mM Tris-HCl pH 7.5, 5 mM dithiothreitol (DTT) 5μMto 20mM metal ion, 10 to 500 μM 4dNTPs, 1 to 500 μM ddNTPs, and 2 unitsof a DNA polymerase. Incubation was at 37° C. for 15 min. The reactionwas stopped by addition of 10μl of 90% formamide, 50 mM EDTA, and 0.1%bromophenol blue.

The resulting samples were heated at 75° C. for two minutes immediatelyprior to loading onto a polyacrylamide gel (8% acrylamide, 0.3%bisacrylamide) in 7M urea, 100 mM Tris-borate, pH 8.9. Electrophoresiswas at 2000 volts for 2 hours. The gel was fixed in 50% methanol, 10%acetic acid for 30 min., dried, and exposed, for autoradiography. Bandintensity in each lane of the resulting film was determined by scanningeach lane with a densitometer. The densitometer used was a double-beamrecording instrument, model MkIIIC (Joyce, Loebl & Co., Ltd.,Gateshead-on-tyne, II, England). Any suitable densitometer instrumentfor scanning gels will also work. Alternatively, the uniformity of theresulting bands can be determined by scanning the DNA products as theyare electrophoresed within the gel.

The ability to incorporate a given ddNTP compared to the correspondingdNTP for any one enzyme is measured as the ratio of ddNTP to dNTPnecessary to allow DNA synthesis that terminates in a fixed range,detected as producing bands of no greater than a fixed molecular weight.That is, the bands produced in the reaction end within a specified rangein the sequencing gel. Thus, if one enzyme discriminates 1000-foldgreater against a given ddNTP compared to another enzyme, a 1000-foldhigher ratio of ddNTP to dNTP will be necessary to obtain bandsterminating at the corresponding sites in the same range of the gel.

Manganese (Mn)

Following is a series of examples of the use of a modified T7 DNApolymerase or the large fragment of E. coli DNA polymerase I in DNAsequencing reactions with Mn present in the sequencing buffer. Theseexamples are not limiting to this invention and are given simply toprovide those skilled in the art with guidelines for use of DNApolymerases of this invention. As described above, those skilled in theart can readily determine other conditions under which DNA polymerasesof this invention can be produced that will give the propertiesdescribed here with respect to uniformity of chain terminating agentincorporation and use in a sequencing reaction.

The specific modified T7 DNA polymerase used in the following exampleswas genetically modified to have no detectable exonuclease activity.This genetically modified DNA polymerase is termed ΔLys 118-Arg 145(Δ28) since the amino acid region from Lys 118 through Arg 145 in T7 DNApolymerase is deleted. The gene encoding this polymerase was constructedin a plasmid pGP5-8 as a variant of the plasmid pGP5-5 as stated in ourcopending application Ser. No. 132,569, was deposited with the ATCC onJan. 13, 1987 and assigned No. 67,287. The specific mutation to pGP5-8was carried out by the same procedure as described for other mutationsin said copending application, that is, by first cloning the T7 gene 5from pGP-3 (Tabor et al., J. Biol. Chem. 282, 1987) into the SmaI andHindIII sites of the vector M13 mp18, to give mGP5-2. (The vector usedand the source of gene 5 are not critical in this procedure.)Single-stranded nGP5-2 DNA was prepared from a strain that incorporatesdeoxyuracil in place of deoxythymidine (Kunkel, Proc. Natl. Acad. Sci.U.S.A. 82, 488, 1985). This procedure provides a strong selection forsurvival of only the synthesized strand (that containing the mutation)when transfected into wild-type E.Coli, since the strand containinguracil will be preferentially degraded. Mutant oligonucleotides, 15-20bases in length, were synthesized by standard procedures. Eacholigonucleotide was annealed to the template, extended using native T7DNa polymerase, and ligated using T4 DNA ligase. Convalently closedcircular molecules were isolated by agarose gel electrophoresis, run inthe presence of 0.5μg/ml ethidium bromide. The resulting purifiedmolecules were then used to transform E. coli 71.18. DNA from theresulting plagues was isolated and the relevant region sequenced toconfirm each mutation.

Referring to FIG. 10, pGP5-8 includes pACYC177 resected at BamHI andHincII sites, T7 DNA from bases 5667 to 6166 containing Φ1.1A and Φ1.1B,and T7 DNA bases 14,306 to 16,869 containing gene 5 with modificationsshown in FIG. 10. pGP5-8 was constructed by first synthesizing the 34mer, 5'CCGGCAAGTTGCCCGGGATGCTCGAGGAGCAGGG 3'. This oligonucleotide wasused as a primer for DNA synthesis on the single-stranded DNA of M13mGP5-2, that contains an insert that encodes T7 gene 5, DNA synthesisand mutant selection was performed as described above. Afterconstruction of the desired mutation in-m-GP5-2, the appropriate regionof T7 gene 5 that contains the 84 bp deletion was inserted into pGP5-5by isolating an EcoRI to HpaI fragment containing T7 DNA from positions14,306 to 15,610, including the region including the 84 bp deletion, andligating it into the comparable region of pGP5-5. The derivative pGP5-8was confirmed to contain the deletion by the presence of the SmaI andXhoI sites that are created by the mutagenesis, and by DNA sequenceanalysis of the region containing the 84 bp deletion pGP5-8 wastransformed into the strain K38/pTrx-3, to create the strainK38/pTrx-3/pGP5-8. Induction of K38/pTrx-3/pGP5-8, and purification ofthe genetically altered T7 DNA polymerase, was carried out using thesame procedure as that described for the analogous strainK38/pTrx-3/pGP5-5 in application Ser. No. 132,569, namely, by infectionof the mutant phage into K38/pGP1-2, as follows. The cells were grown at30° C. to an A₅₉₀ =1.0. The temperature was shifted to 42° C. for 30min., to induce T7 RNA polymerase. IPTG was added to 0.5 mM, and alysate of each phage was added to a moi=10. Infected cells were grown at37° C. for 90 min. The cells were then harvested and extracts preparedby standard procedures for T7 gene 5 protein.

Extracts were partially purified by passage over a phosphocellulose andDEAE A-50 column, and assayed by measuring the polymerase andexonuclease activities directly, as described above. Since thispolymerase has no detectable exonuclease activity chemical modification,as described by Tabor et al., Id., is not necessary before its use in aDNA sequencing reaction. The genetically modified T7 DNA polymerase usedin the examples below was a preparation with an activity of 1000units/ml.

EXAMPLE 1 DNA sequencing Reaction Using Manganese

Standard DNA sequencing reaction methodology is used for sequencing DNAin the presence of Mn. For T7 DNA polymerase the general sequencingsteps are described in detail in Tabor et al., Id. Briefly, the stepsand conditions are as follows:

A. Annealing Reaction

In the annealing reaction the following solution was prepared:

    ______________________________________                                        DNA to be sequenced (e.g., mGPL1-2 DNA)                                                                     7 μl                                         in 10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 2 μg/7 μl                                                      2                                               5X SeqBuf (200 mM Tris-HCl pH 7.5, 5 mM MnCl.sub.2,                           250 mM NaCl)                                                                  Primer (New England Biolabs-17mer, Cat #1210                                                                1                                               0.5 pm/μl)                                                                                              10 μl                                         ______________________________________                                    

This solution was heated at 65° C. 2 min, and slow cooled to roomtemperature.

B. Labeling reaction

In the labeling reaction the following solution was prepared:

    ______________________________________                                        Annealing reaction mixture    10 μl                                        Dithiothreitol 0.1M           1                                               [.sup.35 S]dATP, New England Nuclear NEG-034H                                                               1                                               dTTP, dCTP, dGTP 1.5 μM each                                                                             2                                               Genetically mmodified T7 DNA polymerase, 1 unit/μl                                                       2                                               (ΔLysll8-Arg 145, as described above)                                                                16 μl                                         ______________________________________                                    

This was incubated at room temperature for 5 min.

C. Termination Reaction

In the termination reactions, four reaction mixtures were prepared asfollows:

    ______________________________________                                                       G     A       T       C                                        ______________________________________                                        5X SeqBuf        0.6     0.6     0.6   0.6 μl                              4dNTPs (3 mM)    0.3     0.3     0.3   0.3 μl                              H.sub.2 O        1.9     1.9     1.9   1.9 μl                              ddGTP 0.2 mM (dd=dideoxy)                                                                      0.2 μl                                                    ddATP 0.2 mM             0.2 μl                                            ddTTP 0.2 mM                     0.2 μl                                    ddCTP 0.2 mM                           0.2 ml                                                  3       3       3     3 μl                                ______________________________________                                    

The termination mixtures were incubated at 37° C. for 2 min, and then 3μl aliquots of the completed labeling reaction added to each terminationmixture. The resulting solution was incubated at 37° C. for 5 min.

The termination reactions were stopped with 5 μl of 90% formamide, 20 mMEDTA, 0.2% bromophenol-blue, xylene-cyanol, pH 8.0. The resultingsamples were heated at 75° C. for two minutes, loaded onto apolyacrylamide gel (8% acrylamide, 0.3% bisacrylamide) in 7M urea, 100mM Tris borate pH 8.9, and electrophoresed at 2000 volts for 2 hours.The gel was fixed in 50% methanol, 10% acetic acid for 30 min, dried andused to expose film by autoradiography.

The exposed gel was developed, and the intensity of radioactive bands ineach lane was determined by scanning each lane with a densitometer(Joyce, Loebl & Co., Ltd., model number MkIIIC).

When the same sample is run in the presence of magnesium in place ofmanganese, the underlined bases in the following triplets are 2-5 foldmore intense than adjacent bases whenever these triplets appear: TCT,AAG, GCA, CCT. However, in the example just described, bandscorresponding to every base in all the triplets just shown have the sameintensity, differing by at most 20% from one another.

EXAMPLE 2 Sequencing reaction using manganese, 2X ddGTP and lX ddCTP todifferentiate between G and C by relative band intensities.

In this example, only one vessel was used to perform a sequencingreaction to determine the sequence of two types of bases (namely C andG) in a DNA template. The steps were as follows:

In the annealing reaction the following solution was prepared:

    ______________________________________                                        mGPL-2 DNA (2.7 mM in 10 mM                                                                             8.6 μl                                           Tris-HCl pH 7.5, 0.1 mM EDTA)                                                 5X SeqBuf                 4                                                   Primer (ABI fam primer, 0.4 pm/μl)                                                                   2                                                   H.sub.2 O                 5.4                                                                           20 μl                                            ______________________________________                                    

This solution was heated at 65° C. 2 min, and slow cooled to roomtemperature. The fam primer is labelled with a fluorescent label whichcan be detected as it passes through a sequencing gel, using the ABIModel 370 A DNA Sequencing System.

In the extension reaction the following solution was prepared.

    ______________________________________                                        Annealing reaction mixture                                                                             20 μl                                             Dithiothreitol 0.1M       1                                                   4 dNTP 3 mM               3                                                   ddGTP 30 μM            3                                                   ddCTP 30 μM            1.5                                                                          28.5 μl                                           ______________________________________                                    

This solution was incubated at 37° C. for 2 min, 1.5 μl of geneticallymodified T7 DNA polymerase (Δ28), 1 unit/μ1, added, and the solutionincubated at 37° C., for 10 min. The reaction was stopped by adding 5 μlof 100 mM EDTA, pH 8.0.

The resulting fragments were precipitated as follows: 3.5 μl 3M sodiumacetate, and 100 μl 100% ethanol was added. After incubation on ice for10 min, the mixture was centrifuged for 30 min at 4° C. in amicrocentrifuge. The pellet was washed with 500 μl 70% ethanol, andcentrifuged again for 5 min. The supernatant was decanted, and thepellet dried by centrifuging under vacuum for several minutes. Thesample was then resuspended in 5 μl 90% formamide, 50 mM EDTA pH 8.0,heated at 75° C. for two minutes, and loaded onto an ABI Model 370A DNASequencing System. The instrument was run and the unprocessed (raw) datawas collected as described in the User's Manual for the model 370Ainstrument (Preliminary version, Mar. 1987, Sections 3, 4 and 5).Unprocessed (raw) output for only the fam primer is shown.

The output from this reaction is shown in FIG. 4. Each G is representedby a tall peak and each C by a short one. Thus, the sequence of G's andC's in the DNA is determinable from the peak height. Thus, from onesequencing reaction, with only one label used for all DNA products, aDNA sequence of G's and C's can be determined. Peak height becomesreduced along the length of a gel since products of higher molecularweight are present in lower amounts. However, the difference between anearby G and C remains about 2 fold along the gel, while that of a pairof nearby G's or a pair of nearby C's is approximately uniform (varyingabout 1.1- to 1.4-fold), correcting for the decrease in intensity foreach additional position along the sequence. For example, in FIG. 4 thesignal decreases 2 fold for a given series of bands over a period ofapproximately 60 bases. Thus there is a 1.16% decrease inherent at eachadditional position along the template in this example (since Chi is1.0116 for Chi⁶⁰ =2).

It is important to distinguish between bands of different intensity dueto different efficiency of chain termination within nearby bands, andtwo or more bands migrating together during electrophoresis. The latterevent, called a compression, is an artifact of gel electrophoresis, andnot the DNA sequencing reaction itself, and is not eliminated by usingmanganese. One example of such a compression is marked by an asterisk(*) in FIG. 4. If one knows that such a compression represents theco-migration of two DNA products, as the one noted in FIG. 4, then thatband is an accurate marker of a band of 2X intensity.

The precise sequence in a region of compression cannot be determined. Inorder to determine this sequence, it is necessary either (1) todetermine the sequence in the reverse orientation, (2) run thesequencing gel under stronger denaturing conditions, i.e., highertemperature, or by the addition of 50% formamide, or (3) use anucleotide analog, e.g., dITP or deazaGTP, in place of dGTP.Compressions are due to the formation of stable hairpins in the DNAunder the conditions of gel electrophoresis; incorporation of thesenucleotide analogs destabilize most of these hairpins.

Compressions due to hairpin structures can be of virtually any length,depending on the extent and strength of the hairpin. Thus, with Mn allnearby bands have an approximately equal numbers of DNA products of thesame molecular weight, but do not necessarily have a similar bandintensity due to compressions.

Referring to FIG. 2, the above method was used with just ddGTP in thepresence of manganese at a 1 mM final concentration. Each band on theresulting gel is represented in FIG. 2 as a peak. The intensity of aband is reflected by the height of each peak. With manganese, nearbyband intensity and thus peak height is approximately uniform along thegel, differing between nearby bands by less than 5 or 10%.

In contrast, the output shown in FIG. 3 represents the same experimentrun in the presence of magnesium instead of manganese. Here, nearby bandintensity and thus peak height varies as much as 10 fold.

Referring to FIG. 5, with all four dideoxy nucleotides at equalconcentrations (0.75 μM final concentration for each ddNTP, as inExample 2) in a sequencing reaction in the presence of manganese, nearbybands and corresponding peaks are approximately uniform, varying by nomore than about 1.5-fold again decreasing in absolute intensity for DNAproducts of higher molecular weight. In contrast, in the presence ofmagnesium and all four dideoxy nucleotides at equal concentration, asshown in FIG. 6, nearby band intensity varies greatly.

By varying the concentration of each ddNTP in a sequencing reaction thecomplete nucleotide sequence of a strand of DNA can be determined. Anexample of such a procedure is shown in FIG. 7, where the concentrationof each ddNTP differs by 30% intervals: ddGTP (4.5 μM 2.2x), ddATP (3.0μM, 1.7x), ddTTP (2 μM, 1.3x) and ddCTP (1.4 μM, 1.0x). The DNA sequencedetermined from this graph is shown below the second line in the Figure.Only 6 mistakes (shown by a v ) were made compared to the actual DNAsequence. These mistakes can be eliminated by using greater ratios ofeach ddNTP (e.g., lxddCTP, 2xddTTP, 4xddATP and 8xddGTP). Similarly, bymeasuring peak areas, rather than peak height, the results are moreaccurate. Computer programs to measure such peak areas are readilywritten for existing DNA sequencing machines.

Referring to FIG. 8, the optimum concentration of manganese in asequencing reaction is 1 mM, in the absence of a chelator such ascitrate or isocitrate, compared to 20 mM for magnesium. When 40 mMisocitrate is present in the reaction, the polymerase activity in thepresence of manganese is stimulated 4-fold, and the optimum manganeseconcentration is 5 to 20 mM. Referring to FIG. 9, at 10 mM manganeseconcentration, the optimal isocitrate concentration is 40 mM, resultingin a 4-fold stimulation of polymerase activity. At 10 mM magnesiumconcentration, any amount of isocitrate has an inhibitory effect onpolymerase. These results were obtained by performing polymerasereactions, as described below, in the presence of various chelator andion concentrations. Specifically, reactions (200 μl ) contained 40 mMTris-HCl, pH7.5, 5 mM dithiothreitol, 0.5 mM denatured calf thymus DNA,0.3 mM dGTP, dATP, dCTP and [³ H]dTTP (20 cpm/pm), 50 ug/ml BSA, and theindicated concentrations of MgCl₂, MnCl₂ or sodium isocitrate. Reactionswere begun by the addition of 0.1 unit of genetically modified T7 DNApolymerase (ΔLys118-Arg145). Incubation was 37° C. for 30 min. Reactionswere stopped by the addition of 3 ml of lN HCl and 0.1 M sodiumpyrophosphate, and the acid insoluble radioactivity was determined. Oneunit of DNA polymerase catalyzes the incorporation of 10 nmoles of totalnucleotide into an acid insoluble form in 30 min. under the conditionsof the assay. (Tabor et al. J. Biol Chem. 262, 16212, (1987)).

Pyrophosphatase

When chemically modified T7 DNA polymerase is used for DNA sequencing,specific fragments disappear upon prolonged incubation (Tabor andRichardson, Proc. Nat. Acad. Sci. USA 84:4767, 1987). We refer to thesites where this occurs as "holes" since this process creates a space inthe sequencing gel. The holes occur more frequently when dITP is used inplace of dGTP.

The degradation of specific fragments is an obvious problem in readingDNA sequencing gels. The absence of a fragment is either missedcompletely when the sequence is read, resulting in a deletion in thedetermined sequence, or else a hole is observed that can only beinterpreted as an unknown base at that position.

The current solution to this problem is to keep the reaction timesshort. This is unsatisfactory for two reasons. First, it makes runningthe reactions technically more difficult, since one is forced to workvery rapidly in order to terminate the reactions soon after they arebegun. More importantly, some bands are extremely sensitive to thisdegradation, and disappear even after very short reactions times.

We have constructed a genetically altered form of T7 DNA polymerase(Δ28, described above) that has no detectable level of exonucleaseactivity (<10⁻⁷ the level of the wild type enzyme, or >10,000 timeslower than the chemically modified T7 DNA polymerase). We expected that,since the holes appear with prolonged incubation, they were presumablydue to exonuclease activity, and thus would not occur when thisgenetically modified form of T7 DNA polymerase was used. However, theradioactive fragments mentioned above still disappear at the same ratewhen either chemically or genetically modified T7 DNA polymerase isused.

We have determined that this loss of specific bands is due topyrophosphorolysis activity of the polymerase. This activity is not dueto the exonuclease activity of DNA polymerase, but rather to thereversal of the polymerase activity: in the presence of pyrophosphate(PPi), the polymerase will add PPi to the terminal nucleotide that islocated at the 3 terminus of the chain, in this case releasing adideoxynucleoside 5 triphosphate. See generally Deutscher et al. J.Biol. Chem. 244:3019, 1969; and Kornberg, DNA Replication pp. 125-126,published by Freeman & Co., SF. This reaction has the effect of removingthe block at the 3' terminus, permitting synthesis to extend furtheralong the template. PPi normally accumulates in a DNA synthesis reactionmixture, since it is a product of the polymerization reaction. The siteof pyrophosphorolysis is DNA sequence dependent, and thus the holesdescribed above are produced only at specific sites.

To overcome this problem, the pyrophosphorolysis reaction must beinhibited. One way to inhibit pyrophosphorolysis is to break down thepyrophosphate as it is generated in the polymerase reaction, by addingthe enzyme pyrophosphatase. Other solutions include altering thepyrophosphate by other enzymatic reactions, or preventing thepyrophosphorolysis reaction by the addition of an analog that inhibitsthis activity of the DNA polymerase. We have found that the addition ofeven trace amounts of this enzyme (one thousandth the molar ratio of DNApolymerase molecules) to the sequencing reactions completely stabilizesthe specific class of fragments mentioned above and eliminatesproduction of holes. In the presence of both the genetically alteredform of T7 DNA polymerase (Δ28) and pyrophosphatase, all bands arestable upon even prolonged incubation (up to 2 hours).

For automated sequencing, using differential band intensity, it iscritical that the intensity of every band is determined entirely by theratio of ddNTP to dNTP. Pyrophosphorolysis will create ambiguities bydiminishing the intensity of some bands. Thus, addition ofpyrophosphatase is particularly useful in this sequencing procedure.

Pyrophosphatase should be added whenever chemically or geneticallymodified T7 DNA polymerase or other polymerases are used for sequencing,at at least an amount sufficient to catalyze the hydrolysis, of the PPiformed at a rate that will prevent the accumulation of PPi to a levelthat will lead to pyrophosphorolysis. This is particularly true whendITP is used in place of dGTP, in which case the appearance of holes dueto pyrophosphorolysis reaction occurs to a greater extent.

EXAMPLE 3 Protocol using pyrophosphatase in sequencing reactions

In this example, a normal sequencing protocol was followed. The onlymodification was that yeast inorganic pyrophosphatase was used. Thesource of the pyrophosatase is not important, however in this example weused Sigma yeast inorganic pyrophosphatase catalog number I-4503,without further purification, or further purified on an FPLC mono Qcolumn, and Worthington yeast inorganic pyrophosphatase without furtherpurification. The pyrophosphatase was added to modified T7 DNApolymerase prior to adding the polymerase to the labeling reaction.Typically, 2 units (0.25 μg) of polymerase were used per sequencingreaction set, and 0 001 units of yeast inorganic pyrophosphatase (4 ng).A wide range of pyrophosphatase activity will work successfully: 0.01 ngto 1 μg of yeast pyrophosphatase per sequencing reaction have beentested with success.

For example, in the annealing reaction the following solution wasprepared:

    ______________________________________                                        mGPL-2 DNA (in 10 mM Tris-HCl pH 7.5, 0.1 mM                                                                7 μl                                         EDTA)                                                                         5X SeqBuf                     2                                               Primer (New England Biolabs-17mer,                                                                         1                                                0.5 pm/μl Cat #1211)      10 μl                                         ______________________________________                                    

This solution was heated at 65° C. 2 min, and slow cooled to roomtemperature.

In the labeling reaction the following solution was prepared:

    ______________________________________                                        Annealing reaction mixture   10 μl                                         Dithiothreitol 0.1M           1                                               .sup.35 S dATP, New England Nuclear NEG-034H                                                                1                                               3 dNTP (1.5 μM each dTTP, dCTP, 3 μM dITP)                                                            2                                               Enzyme mixture (see below)    2                                                                            16 μl                                         ______________________________________                                        Enzyme mixture:                                                               Genetically modified T7 DNA polymerase,                                                               1 unit/μl                                          Δ Lys118-Arg145                                                         Yeast inorganic pyrophosphatase                                                                       0.01 units μl                                      in 20 mM Tris-HCl pH 7.5, 10 mM                                               β-mercaptoethanol,                                                       50 μg/ml bovine serum albumin                                              ______________________________________                                    

This solution was incubated at room temperature for 5 min.

In the termination reactions the following four reaction mixtures wereprepared:

    ______________________________________                                                       G     A       T       C                                        ______________________________________                                        5X SeqBuf (see above)                                                                          0.6     0.6     0.6   0.6 μl                              4dNTPs (3mM each dATP,                                                                         0.3     0.3     0.3   0.3 μl                              dTTP, dCTP, and 6 mM dITP)                                                    H.sub.2 O        1.9     1.9     1.9   1.9 μl                              ddGTP 0.03 mM    0.2 μl                                                    ddATP 0.2 mM             0.2 μl                                            ddTTP 0.2 mM                     0.2 μl                                    ddCTP 0.2 mM                           0.2 ml                                                  3       3       3     3 μl                                ______________________________________                                    

These termination mixtures were incubated at 37° C for 2 min, and 3 μlaliquots of the labeling reaction added to each termination mixture. Theresulting solutions were incubated at 37° C. for 60 min.

Each termination reaction was stopped with 5 μl of 90% formamide, 20 mMEDTA, 0.2% bromophenol-blue, xylene-cyanol, pH 8.0.

The resulting samples were heated at 75° C. for two minutes, loaded ontoa polyacrylamide gel (8% polyacrylamide, 0.3% bisacrylamide) in 7M urea,100 mM Tris-borate, pH 8.9, and electrophoresed at 2000 volts for 2hours. The gel was fixed in 50% methanol, and 10% acetic acid for 30min, dried, and used to expose film by autoradiography.

Apparatus

Referring to FIG. 11, apparatus 100, suitable for automated DNAsequencing, includes a reactor 102 including the above describedreagents 104, for example, DNA polymerase, manganese or iron ions,chelators and pyrophosphatase. The apparatus is also provided with a elbox 106, for separating DNA products according to their molecularweights, and a gel reading means 108 for detecting the DNA products asthey pass through the gel (shown by dashed arrows 107). ). Further, acomputing means 110 is provided to calculate the intensity of bands ofDNA products, and the position of the bands relative to one another. Ifthe DNA products are run in one lane, then the computer means is able tocompute the DNA sequence from the band intensity and position. Standardcomputer programs are used to perform this function.

Other embodiments are within the following claims.

We claim:
 1. A method for sequencing a strand of DNA, comprising thesteps of:providing said strand hybridized with a primer able tohybridize to said strand, to give an hybridized mixture, incubating saidhydridized mixture with four deoxyribonucleoside triphosphates, a DNApolymerase, and a first chain terminating agent, wherein said DNApolymerase causes said primer to be elongated to form a first series offirst DNA products differing in the length of the elongated primer, eachsaid first DNA product having a said chain terminating agent at itselongated end, the number of molecules of each said first DNA productsbeing approximately the same for substantially all DNA productsdiffering in length by no more than 20 bases, and providing a secondchain terminating agent in said hybridized mixture at a concentrationdifferent from said first chain terminating agent, wherein said DNApolymerase causes production of a second series of second DNA productsdiffering in the length of the elongated primer, each said second DNAproduct having said second chain terminating agent at its elongated end,the number of molecules of each said second DNA products beingapproximately the same for substantially all second DNA productsdiffering in length from each other by from 1 to 20 bases, and beingdistinctly different from the number of molecules of all said first DNAproducts having a length differing by no more than 20 bases from that ofsaid second DNA products.
 2. The method of claim 1 further including thesteps of:separating said first and second DNA products by gel permeationaccording to molecular weight to form a first and second series of bandsrespectively, each said first or second series band representing a saidfirst or second DNA product, respectively, of a given molecular weight,wherein the intensity of each nearby first series band is approximatelythe same for substantially all said first series bands, and wherein theintensity of substantially all nearby second series bands isapproximately the same, and wherein the intensity of substantially allbands of the first series is distinctly different from the intensity ofeach nearby band of the second series, and determining the position andintensity of each said first and second series band.
 3. The method ofclaim 1 further comprising the step of:providing a third chainterminating agent in said hybridized mixture at a concentrationdifferent from said first and second chain terminating agents, whereinsaid polymerase causes production of a third series of third DNAproducts differing in the length of the elongated primer, each saidthird DNA product having said third chain terminating agent at itselongated end, the number of molecules of each said third DNA productbeing approximately the same for substantially all said third DNAproducts which differ in length by no more than 20 bases, wherein thenumbers of molecules of substantially all said first, all said secondand all said third DNA products are distinctly different from thenumbers of molecules of all those DNA products of a different serieswhich are of lengths differing from them by no more than 20 bases. 4.The method of claim 3 further including the steps of:separating saidfirst, second and third DNA products by gel permeation according tomolecular weight to form a first, second and third series of bands,respectively, each said first, second or third series band representinga said first, second or third DNA product, respectively, of a givenmolecular weight, wherein the intensity of each nearby first series bandis approximately the same for substantially all said first series bands,wherein the intensity of substantially all nearby second series bands isapproximately the same, and the intensity of substantially all nearbythird series bands is approximately the same, and wherein the intensityof substantially all nearby bands of different series is distinctlydifferent, and determining the position and intensity of each said band.5. The method of claim 3 further comprising the step of:providing insaid hybridized mixture a fourth chain terminating agent at aconcentration different from said first, second and third chainterminating agents, wherein said DNA polymerase causes production of afourth series of fourth DNA products differing in the length of theelongated primer, each said fourth DNA product having said fourth chainterminating agent at its elongated end, the number of molecules of eachsaid fourth DNa product being approximately the same or substantiallyall fourth DNa products differing in length by no more than 20 bases,wherein the number of molecules of substantially all said first, allsaid second, all said third, and all said fourth series of DNA productsis distinctly different from all the number of molecules of those DNaproducts of a different series which differ in length from them by nomore than 20 bases.
 6. The method of claim 5, further including thesteps of:separating said first, second, third and fourth DNA products bygel permeation according to molecular weight to form a first, secondthird and fourth series of bands respectively, each said first, second,third and fourth series band representing a said first, second, third orfourth DNA product of a given molecular weight, wherein each saidsecond, third and fourth series produce second, third and fourth bands,wherein the intensity of substantially all nearby first series bands, orsubstantially all nearby second series bands, or substantially allnearby third series bands, or substantially all nearby fourth seriesbands is approximately the same, and wherein the intensity ofsubstantially all nearby bands in a different series is distinctlydifferent, and determining the position and intensity of each said band.7. The method of claim 1, 2, 3, 4, 5 or 6 wherein said hybridizedmixture is provided with a manganese or iron ion, wherein said ioncauses said polymerase to be non-discriminatory for a said chainterminating agent.
 8. The method of claim 5 wherein said DNA productsare separated according to molecular weight in less than four lanes of agel.
 9. The method of claim 8 wherein the intensity of each band ismeasured by a gel reading apparatus.
 10. The method of claim 1, 2, 3, 4,5, or 6 wherein each said chain terminating agent is a dideoxynucleosidetriphosphate.
 11. The method of claim 7, wherein said hybridized mixtureis provided with a chelator.
 12. The method of claim 11, said chelatorbeing citrate or isocitrate.
 13. A method for sequencing a strand ofDNA, comprising the steps of:providing a DNA polymerase, and incubatingsaid polymerase and said strand of DNA in a solution comprising amanganese ion and a chain terminating agent wherein said ion is providedat a concentration effective for causing production of approximatelyequal numbers of molecules of these DNA products which differ in sizefrom each other by no more than 20 bases.
 14. A kit for sequencing DNAcomprising:a first container comprising a DNA polymerase, a secondcontainer comprising a chain terminating agent, and a compoundcomprising a manganese ion.
 15. A kit for sequencing DNA comprising:afirst container comprising a DNA polymerase, a second containercomprising a chain terminating agent, and a compound comprising an ironion.
 16. The kit of claim 14 or 15 wherein said polymerase is a T7-typeDNA polymerase, suitable for DNA sequencing, Klenow, or Taq polymerase.17. The kit of claim 14, 16, or 15, wherein each said chain terminatingagent is a dideoxynucleoside triphosphate.
 18. The kit of claim 16further comprising a deoxyribonucleoside triphosphate.
 19. The kit ofclaim 14 further comprising a chelator.
 20. The kit of claim 19, saidchelator being citrate or isocitrate.
 21. A method for sequencing DNAcomprising:providing a DNA polymerase in a reaction medium in which saidDNA polymerase is substantially non-discriminating for a chainterminating agent, and incubating said DNA in said reaction medium withsaid DNa polymerase, a primer, four deoxyribonucleosie triphosphates anda chain terminating agent to elongate said primer to form a series ofDNA products differing in the length of the elongated primer and havingsaid chain terminating agent at the elongated end, the number ofmolecules of each said DNA product being approximately the same forsubstantially all those DNA products differing in size by no more than20 bases.
 22. The method of claim 21 wherein said DNA polymerase is aT7-type DNA polymerase provided in a solution comprising manganese ions.23. The method of claims 7, 13, or 22 wherein said manganese ions are ata concentration between 5 μM and 20 μM.
 24. A method for sequencing astrand of DNA, comprising the steps of:providing said strand hybridizedwith a primer able to hybridize to said strand, to give a hybridizedmixture, and incubating said hybridized mixture with fourdeoxyribonucleoside triphosphates, a DNA polymerase, and a plurality ofchain terminating agents in a reaction medium in which said polymerasecauses said primer to be elongated to form a series of DNA productsdiffering in the length of the elongated primer, each DNA product havinga first said chain terminating agent at its elongated end, wherein thenumber of molecules of said DNA products is approximately the same forsubstantially all DNA products differing in length by no more than 20bases.
 25. The method of claim 24, wherein said reaction mediumcomprises manganese ions.
 26. The method of claim 25, wherein saidmanganese ions are at a concentration between 5 μM and 20 mM.
 27. Themethod of claim 25, wherein said reaction medium comprises a chelatorand manganese ions at a concentration between 0.005 and 100 mM.
 28. Themethod of claim 13 wherein said solution comprises a chelator and saidmanganese ion is at a concentration between 0.005 nd 100 mM.
 29. Themethod of claim 13 wherein said manganese ion is at a concentrationbetween 5 μM and 20 mM.
 30. The method of claim 1, 2, 3, 4, 5 or 6,wherein said hybridized mixture is provided with a manganese ion,wherein said ion causes said polymerase to be non-discriminating for asaid chain terminating agent.
 31. The method of claim 1, 2, 3, 4, 5 or6, wherein said DNA polymerase is selected from the group consisting ofthe large fragment of E. coli DNA polymerase I and Taq polymerase. 32.The method of claim 1, 2, 3, 4, 5 or 6, wherein said DNA polymerase is aT7-type DNA polymerase.
 33. A method for sequencing a strand of DNA,comprising the steps of:providing a DNA polymerase, and incubating saidpolymerase and said strand of DNA in a solution comprising an iron ionand a chain terminating agent wherein said ion is provided at aconcentration effective for causing production of approximately equalnumbers of molecules of DNA products differing in size by no more than20 bases.
 34. A method for sequencing a strand of DNA, comprising thesteps of:providing said strand hybridized with a primer able tohybridize to said strand to give an hybridized mixture, incubating saidhybridized mixture with four deoxyribonucleoside triphosphates, a DNApolymerase, and a plurality of different chain terminating agents eachcapable of terminating the DNa synthesis at a different nucleotide base,to cause said primer to be elongated to form a series of DNA productsdiffering in length with each DNA product having a chain terminatingagent at its elongated end, the amount of each said chain terminatingagent being distinctly different from that of each other chainterminating agent, and said incubation causing the total amount of saidseries terminating with one chain terminating agent to be distinctlydifferent from the total amount of said series terminating with eachdifferent chain terminating agent, and separating said series accordingto length, whereby the DNA products of approximately the same lengthcontaining one chain terminating agent are distinctly different inamount from those containing any other chain terminating agent.